ClonoMatch: a tool for identifying homologous immunoglobulin and T-cell receptor sequences in large databases
| العنوان: | ClonoMatch: a tool for identifying homologous immunoglobulin and T-cell receptor sequences in large databases |
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| المؤلفون: | Taylor Jones, Luke Myers, Samuel Day, Cinque Soto, James E. Crowe |
| المصدر: | Bioinformatics |
| بيانات النشر: | Oxford University Press (OUP), 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | Statistics and Probability, Computer science, Sequence analysis, Somatic cell, B-cell receptor, Computational biology, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Homologous chromosome, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, T-cell receptor, Applications Notes, Dna rearrangements, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, chemistry, biology.protein, Antibody, DNA, 030215 immunology |
| الوصف: | Summary B-cell receptor (BCR) and T-cell receptor (TCR) repertoires are generated through somatic DNA rearrangements and are responsible for the molecular basis of antigen recognition in the immune system. Next-generation sequencing (NGS) of DNA and the falling cost of sequencing due to continued development of these technologies have made sequencing assays an affordable way to characterize the repertoire of adaptive immune receptors (sometimes termed the ‘immunome’). Many new workflows have been developed to take advantage of NGS and have placed the resulting immunome datasets in the public domain. The scale of these NGS datasets has made it challenging to search through the Complementarity-determining region 3 (CDR3), which is responsible for imparting specific antibody-antigen interactions. Thus, there is an increasing demand for sequence analysis tools capable of searching through CDR3s from immunome data collections containing millions of sequences. To address this need, we created a software package called ClonoMatch that facilitates rapid searches in bulk immunome data for BCR or TCR sequences based on their CDR3 sequence or V3J clonotype. Availability and implementation Documentation, software support and the codebase are all available at https://github.com/crowelab/clonomatchTest. This software is distributed under the GPL v3 license. |
| تدمد: | 1460-2059 1367-4803 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::75404638ebd2acb3369df18545eae12cTest https://doi.org/10.1093/bioinformatics/btaa1028Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....75404638ebd2acb3369df18545eae12c |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14602059 13674803 |
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